28MQ: UBA6-FAT10Dha-UBE2Z trapped ternary complex

Cryo-EM structure of UBA6-FAT10Dha-UBE2Z trapped ternary complex. Determined by electron microscopy at 3.04 Å resolution. Released 23 Sept 2026.

Method: Electron microscopy
Resolution: 3.04 Å
Organism: Homo sapiens
Chains: 3
Atoms: 11,201
Mol. weight: 175.97 kDa
Ligands: IHP
Released: 23 Sept 2026

Explore 28MQ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

28MQ contains 80 α-helices and 73 β-strands across 3 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 16 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	85-87	3
α-helix	89-91	3
α-helix	98-113	16
α-helix	115-116	2
β-strand	119-123	5	1
β-strand	130-136	7	1
α-helix	137-138	2
β-strand	147-153	7	1
β-strand	164-167	4	1
β-strand	178	1	2
β-strand	181	1	2
β-strand	186	1	1
β-strand	187	1	2
α-helix	190-192	3
α-helix	206-214	9
α-helix	221-224	4
α-helix	237-249	13
α-helix	250-255	6
α-helix	256-257	2
α-helix	265-287	23
α-helix	290-292	3
α-helix	295	1
β-strand	296	1	3
α-helix	297	1
β-strand	307	1	3
α-helix	310-329	20

Chain B: 58 helices, 49 β-strands

Element	Residues	Length	Sheet
α-helix	46-59	14
β-strand	63-67	5	4
α-helix	71-83	13
β-strand	87-91	5	4
β-strand	95	1	5
α-helix	98-102	5
α-helix	109-114	6
β-strand	117	1	5
α-helix	118-127	10
β-strand	134-138	5	4
α-helix	148-153	6
β-strand	156-160	5	4
α-helix	164-174	11
α-helix	180-181	2
β-strand	182-189	8	4
β-strand	190	1	6
β-strand	192-198	7	4
β-strand	202-205	4	7
α-helix	212-214	3
β-strand	215-217	3	8
β-strand	218-222	5	9
β-strand	227-231	5	9
α-helix	232	1
β-strand	244-248	5	8
α-helix	254-256	3
β-strand	257	1	8
β-strand	260-262	3	8
β-strand	264-267	4	9
β-strand	270-273	4	9
α-helix	280-282	3
β-strand	287-291	5	8
β-strand	295-298	4	7
α-helix	303-305	3
α-helix	321-339	19
α-helix	342-344	3
α-helix	348-364	17
α-helix	369-372	4
α-helix	373-381	9
β-strand	386	1	6
α-helix	388-407	20
α-helix	411-413	3
β-strand	417	1	4
β-strand	420	1	4
α-helix	422-426	5
α-helix	433-435	3
α-helix	444-459	16
β-strand	462-466	5	10
α-helix	470-482	13
β-strand	492-496	5	10
β-strand	500	1	11
α-helix	505-508	4
α-helix	514-516	3
β-strand	520	1	11
α-helix	521-532	12
β-strand	538-541	4	10
α-helix	547-549	3
α-helix	555-560	6
β-strand	563-566	4	10
α-helix	571-582	12
β-strand	588-594	7	10
β-strand	597-603	7	10
β-strand	608	1	12
α-helix	611-613	3
α-helix	616-620	5
α-helix	624-628	5
α-helix	634-646	13
α-helix	647-651	5
α-helix	652-662	11
α-helix	666-674	9
α-helix	682-690	9
α-helix	696-708	13
α-helix	709-713	5
α-helix	714-721	8
β-strand	727	1	13
β-strand	733	1	13
α-helix	752-768	17
α-helix	775-778	4
α-helix	780-787	8
α-helix	819-833	15
α-helix	840-842	3
α-helix	858-872	15
α-helix	880-887	8
α-helix	890-892	3
α-helix	895-914	20
α-helix	918-920	3
β-strand	922-927	6	10
β-strand	932-937	6	10
α-helix	938-939	2
β-strand	940	1	12
α-helix	941	1
β-strand	944-945	2	14
α-helix	947-949	3
β-strand	951-952	2	14
β-strand	958-961	4	15
β-strand	967	1	16
α-helix	968-979	12
β-strand	983	1	17
β-strand	988	1	18
β-strand	991	1	18
α-helix	1003-1006	4
β-strand	1008	1	16
α-helix	1009-1013	5
β-strand	1021-1024	4	15
β-strand	1027-1028	2	17
α-helix	1036-1037	2
β-strand	1038-1039	2	17
β-strand	1043-1046	4	15

Chain C: 6 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	9-13	5	19
β-strand	20-23	4	19
β-strand	29	1	20
α-helix	30-41	12
α-helix	45-47	3
β-strand	48-52	5	19
β-strand	55-56	2	19
β-strand	62	1	20
α-helix	63-66	4
β-strand	73-80	8	19
β-strand	88-93	6	21
β-strand	101-106	6	21
β-strand	111	1	22
α-helix	112-123	12
α-helix	127-129	3
β-strand	131-134	4	21
β-strand	137-138	2	21
β-strand	144	1	22
α-helix	145-148	4
β-strand	155-159	5	21

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin-conjugating enzyme E2 Z	A	protein	356	Homo sapiens	Q9H832 (AlphaFold model)
Ubiquitin-like modifier-activating enzyme 6	B	protein	1054	Homo sapiens	A0AVT1 (AlphaFold model)
Ubiquitin D	C	protein	167	Homo sapiens	O15205 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>28MQ_1 Ubiquitin-conjugating enzyme E2 Z (chains A)
GPMAESPTEEAATAGAGAAGPGASSVAGVVGVSGSGGGFGPPFLPDVWAAAAAAGGAGGP
GSGLAPLPGLPPSAAAHGAALLSHWDPTLSSDWDGERTAPQCLLRIKRDIMSIYKEPPPG
MFVVPDTVDMTKIHALITGPFDTPYEGGFFLFVFRCPPDYPIHPPRVKLMTTGNNTVRFN
PNFYRNGKVCLSILGTWTGPAWSPAQSISSVLISIQSLMTENPYHNEPGFEQERHPGDSK
NYNECIRHETIRVAVCDMMEGKCPCPEPLRGVMEKSFLEYYDFYEVACKDRLHLQGQTMQ
DPFGEKRGHFDYQSLLMRLGLIRQKVLERLHNENAEMDSDSSSSGTETDLHGSLRV

Sequence of entity 2 (B), FASTA

>28MQ_2 Ubiquitin-like modifier-activating enzyme 6 (chains B)
GPMEGSEPVAAHQGEEASCSSWGTGSTNKNLPIMSTASVEIDDALYSRQRYVLGDTAMQK
MAKSHVFLSGMGGLGLEIAKNLVLAGIKAVTIHDTEKCQAWDLGTNFFLSEDDVVNKRNR
AEAVLKHIAELNPYVHVTSSSVPFNETTDLSFLDKYQCVVLTEMKLPLQKKINDFCRSQC
PPIKFISADVHGIWSRLFCDFGDEFEVLDTTGEEPKEIFISNITQANPGIVTCLENHPHK
LETGQFLTFREINGMTGLNGSIQQITVISPFSFSIGDTTELEPYLHGGIAVQVKTPKTVF
FESLERQLKHPKCLIVDFSNPEAPLEIHTAMLALDQFQEKYSRKPNVGCQQDSEELLKLA
TSISETLEEKPDVNADIVHWLSWTAQGFLSPLAAAVGGVASQEVLKAVTGKFSPLCQWLY
LEAADIVESLGKPECEEFLPRGDRYDALRACIGDTLCQKLQNLNIFLVGCGAIGCEMLKN
FALLGVGTSKEKGMITVTDPDLIEKSNLNRQFLFRPHHIQKPKSYTAADATLKINSQIKI
DAHLNKVCPTTETIYNDEFYTKQDVIITALDNVEARRYVDSRCLANLRPLLDSGTMGTKG
HTEVIVPHLTESYNSHRDPPEEEIPFCTLKSFPAAIEHTIQWARDKFESSFSHKPSLFNK
FWQTYSSAEEVLQKIQSGHSLEGCFQVIKLLSRRPRNWSQCVELARLKFEKYFNHKALQL
LHCFPLDIRLKDGSLFWQSPKRPPSPIKFDLNEPLHLSFLQNAAKLYATVYCIPFAEEDL
SADALLNILSEVKIQEFKPSNKVVQTDETARKPDHVPISSEDERNAIFQLEKAILSNEAT
KSDLQMAVLSFEKDDDHNGHIDFITAASNLRAKMYSIEPADRFKTKRIAGKIIPAIATTT
ATVSGLVALEMIKVTGGYPFEAYKNCFLNLAIPIVVFTETTEVRKTKIRNGISFTIWDRW
TVHGKEDFTLLDFINAVKEKYGIEPTMVVQGVKMLYVPVMPGHAKRLKLTMHKLVKPTTE
KKYVDLTVSFAPDIDGDEDLPGPPVRYYFSHDTD

Sequence of entity 3 (C), FASTA

>28MQ_3 Ubiquitin D (chains C)
GPMAPNASTLTVHVRSEEWDLMTFDANPYDSVKKIKEHVRSKTKVPVQDQVLLLGSKILK
PRRSLSSYGIDKEKTIHLTLKVVKPSDEELPLFLVESGDEAKRHLLQVRRSSSVAQVKAM
IETKTGIIPETQIVTLNGKRLEDGKMMADYGIRKGNLLFLASYSIGA

Ligands and cofactors

ID	Name	Formula	Copies
IHP	Inositol hexakisphosphate	C6 H18 O24 P6	1

Primary citation

Structural determinants for FAT10 activation and transfer from UBA6 to E2 enzymes. Ellison, C.J., Riechmann, C., Dalietou, E.V. et al. Nat Commun (2026) 17. DOI 10.1038/s41467-026-76603-3 · PubMed

Other PDB entries of the same protein (UniProt Q9H832 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5A4P 2.1 Å, Structure of UBE2Z provides functional insight into specificity in the FAT10 conjugation…
9YKV 2.73 Å, Cryo-EM structure of double-loaded human UBA6-UBE2Z-FAT10(t)/FAT10(a) thioester mimetic…
28MO 3.01 Å, Cryo-EM structure of UBA6-UbDha-UBE2Z trapped ternary complex (singly loaded)
28MP 3.12 Å, Cryo-EM structure of UBA6-UbDha-UBE2Z trapped ternary complex (doubly loaded)
9YLF 3.14 Å, Cryo-EM structure of single-loaded human UBA6-UBE2Z/Ub(a) adenylate complex.
9YLB 3.24 Å, Cryo-EM structure of single-loaded human UBA6-UBE2Z/FAT10(a) adenylate complex.
9YKW 3.86 Å, Cryo-EM structure of double-loaded human UBA6-UBE2Z-Ub(t)/Ub(a) thioester mimetic complex.

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